run test with small whitelist for dual indexes (39e91d41) · Commits · github_fork / Universc

test/run_tests_sciseq_local.sh

+16 −21

Original line number	Diff line number	Diff line
		@@ -21,20 +21,21 @@ fi

		##unpigz -k test/shared/sciseq-v3-test/SRR7827205*fastq.gz

		if [ -f test/shared/sciseq-v3-test/SRR7827205_S1_L001_R1_001.fastq ]; then
		rename "s/_S1_L001/_L001/" test/shared/sciseq-v3-test/SRR7827205_S1_L001_R1_001.fastq*
		fi
		if [ -f test/shared/sciseq-v3-test/SRR7827205_S1_L001_R1_001.fastq ]; then
		rename "s/_S1_L001/_L001/" test/shared/sciseq-v3-test/SRR7827205_S1_L001_R1_001.fastq*
		fi
		if [ -f test/shared/sciseq-v3-test/SRR7827205_S2_L002_R1_001.fastq ]; then
		rename -n "s/_S2_L002/_L002/" test/shared/sciseq-v3-test/SRR7827205_S2_L002_R1_001.fastq*
		fi
		if [ -f test/shared/sciseq-v3-test/SRR7827205_S2_L002_R2_001.fastq ]; then
		rename -n "s/_S2_L002/_L002/" test/shared/sciseq-v3-test/SRR7827205_S2_L002_R2_001.fastq*
		fi
		if [ -d test-icell8-72618-KU812-2-lanes ];then
		rm -rf test-icell8-72618_KU812-2-lanes
		mv test/shared/sciseq-v3-test/SRR7827205_S1_L001_R1_001.fastq.gz test/shared/sciseq-v3-test/SRR7827205_S1_R1.fastq.gz
		mv test/shared/sciseq-v3-test/SRR7827205_S1_L001_R2_001.fastq.gz test/shared/sciseq-v3-test/SRR7827205_S1_R2.fastq.gz
		mv test/shared/sciseq-v3-test/SRR7827205_S1_L001_I1_001.fastq.gz test/shared/sciseq-v3-test/SRR7827205_S1_I1.fastq.gz
		mv test/shared/sciseq-v3-test/SRR7827205_S1_L001_I2_001.fastq.gz test/shared/sciseq-v3-test/SRR7827205_S1_I2.fastq.gz

		#if [ -f test/shared/sciseq-v3-test/SRR7827205_S1_L001_R1_001.fastq ]; then
		# rename "s/_S1_L001/_S1/" test/shared/sciseq-v3-test/SRR7827205_S1_L001_R1_001.fastq*
		# rename "s/_001//" test/shared/sciseq-v3-test/SRR7827205_S1_R1_001.fastq*
		#fi
		#if [ -f test/shared/sciseq-v3-test/SRR7827205_S1_L001_R2_001.fastq ]; then
		# rename "s/_S1_L001/_S1/" test/shared/sciseq-v3-test/SRR7827205_S1_L001_R2_001.fastq*
		# rename "s/_001//" test/shared/sciseq-v3-test/SRR7827205_S1_R2_001.fastq*
		#fi
		if [ -d test-sciseq ];then
		rm -rf test-sciseq
		fi

		if [[ ! -f whitelists/sciseq3_barcode_test.txt ]]; then
		@@ -49,12 +50,6 @@ bash launch_universc.sh --id "test-sciseq" --technology "sciseq" \
		--barcodefile whitelists/sciseq3_barcode_test.txt \
		--jobmode "local" --localcores 1 --verbose

		bash launch_universc.sh --id "test-sciseq" --technology "sciseq" \
		--reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \
		--read1 "test/shared/sciseq-v3-test/SRR7827205_S1_R1.fastq.gz" \
		--read2 "test/shared/sciseq-v3-test/SRR7827205_S1_R2.fastq.gz" \
		--jobmode "local" --localcores 1

		if [ -f test/shared/sciseq-v3-test/SRR7827205_S1_L001_R1_001.fastq.gz ]; then
		rename "s/_S1_L001/_S1/" test/shared/sciseq-v3-test/SRR7827205_S1_L001_[IR][12]_001.fastq*
		rename "s/_001//" test/shared/sciseq-v3-test/SRR7827205_S1_[IR][12]_001.fastq*

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